Sequence
atgc intronic sequence ATGC exonic sequence...tttcttttcagagctatttttttgaaaaaaaatcaagccagaaatatttgtacaaataaggtttatcatgagccattgttttgtccttctgtacgtacagAGAACTTGCTGTTGACCGCAGACCAGAGAACAGTCAAGCTTGTTGACCTTGGTTTAGCAAGAGAAGAGACATTAACAGAGATGATGACTGCAGAGACAGG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g38080.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g38080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G165231_T01 (Zea mays), 3'ss of exon 3
tttcttttcagagctatttttttgaaaaaaaatcaagccagaaatatttgtacaaataaggtttatcatgagccattgttttgtccttctgta-cgtacagAGAACTTGCTGTTGACCGCAGACCAGAGAACAGTCAAGCTTGTTGACCTTGGTTTAGCAAGAGAAGAGACATTAACAGAGATGATGACTGCAGAGACAGG
| |||| | | || | | || |||| | || || | || | || | | | | ||| |||| | |||||| || | | ||| ||||||| || || |||| ||||||||||||||||| || |||||||| |||||||| || || ||||||||| |||| |||||||||||||| ||||||||
aatttttttcgtcccatgtcatcttttaagaatcta-ccggacagatatctattcagactgatgatcttgagtccgtgttttcccccttcatttcgtgcagAGAATCTGTTGCTGACTGCAGACCAGAGAACAGTAAAACTTGTTGATCTTGGTTTGGCTAGGGAAGAGACACTAACGGAGATGATGACTGCTGAGACAGG
upper sequence: LOC_Os02g38080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G07490.1 (Glycine max), 3'ss of exon 3
tttcttttcagagctatttttttgaaaaaaaatcaagccagaaatatttgtacaaataaggtttatcatgagccattgttt--tgtccttctgtacgtacagAGAACTTGCTGTTGACCGCAGACCAGAGAACAGTCAAGCTTGTTGACCTTGGTTTAGCAAGAGAAGAGACATTAACAGAGATGATGACTGCAGAGACAGG
| | | | | |||| || ||| | | | | || | | || | | | | || | |||||| | | |||| |||||| | ||||| | ||| || | ||| || || |||| ||| | ||| |||| ||||||||| | |||||||||||||||||||| ||||||||
aaacagcttctaattgcataattgataat--atctatctatttcttttcttttcatcaatgatcaagtgtaattcttatcacgtgtcctggtttcatcccagATAACTTGATCTTGACAGAAGATCATAAAACTGTTAAACTTGCTGATTTCGGTCTAGCCAGAGAAGAGTCCTTAACAGAGATGATGACTGCTGAGACAGG
upper sequence: LOC_Os02g38080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G18730.1 (Glycine max), 3'ss of exon 3
--tttcttttcagagctatttttttgaaaaaaaatcaagc-cagaaatatttg-tacaaataaggtttatcatgagccattgttttgtccttctgtacgtacagAGAACTTGCTGTTGACCGCAGACCAGAGAACAGTCAAGCTTGTTGACCTTGGTTTAGCAAGAGAAGAGACATTAACAGAGATGATGACTGCAGAGACAGG
||| | | | ||||||| || || | | | || | | | || | | ||| ||||| || |||| | | || || |||||| |||||||| ||||| | |||||||| |||||||||||| | || |||||||||||||||||||| ||||||| |||||||||||||| ||||| ||
ttgttcagtatatacgcattttttatcaattgtataactcgcccaagtgtaaaacatcaacataatgtat-atgagg-atccttttattttcctcta--tacagATAACTTGCTATTGACTGAAGACCAGAAAACAGTCAAGCTAGCGGATTTTGGTTTAGCAAGAGAAGAGTCATTAACTGAGATGATGACTGCTGAGACGGG
upper sequence: LOC_Os02g38080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA04G36210.1 (Glycine max), 3'ss of exon 3
--tttcttttcagagctatttttttgaaaaaaaatcaagccagaaatatttgtacaaata-aggtttatcatgagccattgttttgtccttctgtacgtacagAGAACTTGCTGTTGACCGCAGACCAGAGAACAGTCAAGCTTGTTGACCTTGGTTTAGCAAGAGAAGAGACATTAACAGAGATGATGACTGCAGAGACAGG
|| | |||| ||||| || | ||| | ||| || | | | |||| || |||| | | || || |||||| |||||||| ||||| | |||||||| |||||||||||| | || |||||||||||||||||||| ||||||| |||||||||||||| || |||||
agttgttaacttaagcttctttttctcctttgtataacttgccaaagtgtcaaacatctacataatgaatatgaag-atccttttattttcctcta--tacagATAACTTGCTATTGACTGAAGACCAGAAAACAGTCAAGCTAGCAGATTTTGGTTTAGCAAGAGAAGAGTCATTAACTGAGATGATGACTGCTGAAACAGG
upper sequence: LOC_Os02g38080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G08500.1 (Glycine max), 3'ss of exon 3
tttcttttcagagctatttttttgaaaaaaaatcaagccagaaatatt-tgtacaaataaggtttatcatgagccat-tgttttgtccttctgtacgtacagAGAACTTGCTGTTGACCGCAGACCAGAGAACAGTCAAGCTTGTTGACCTTGGTTTAGCAAGAGAAGAGACATTAACAGAGATGATGACTGCAGAGACAGG
| | || | | | || | ||| | | | || | | || | | | | | | | | | | |||||| | | |||| |||||| | ||||| | ||| || | | |||| || || | || | ||| |||| ||||||||| | |||||||||||||||||||| ||||||||
--cataattgataataataatattaagcactatctgtctatttcttttctattcatcaatgatcaagtgtaattcttatcatgtgtcctgttttcatcccagATAACTTGATCTTGACAGAAGATCATAAAGCAGTTAAACTAGCCGATTTCGGTCTAGCCAGAGAAGAGTCCTTAACAGAGATGATGACTGCTGAGACAGG
upper sequence: LOC_Os02g38080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G50180.1 (Arabidopsis thaliana), 3'ss of exon 3
------tttcttttcagagctatt--tttttgaaaaaaaatcaagccagaaatatttgtac-aaataaggtttatcatgagccattgttttgtccttctgtacgtacagAGAACTTGCTGTTGACCGCAGACCAGAGAACAGTCAAGCTTGTTGACCTTGGTTTAGCAAGAGAAGAGACATTAACAGAGATGATGACTGCAGAGACAGG
|| || || || | || | || ||| || | || || | ||| | | || | |||||| ||| | ||||||||||||| || || |||||||| | |||||| || || | || |||| ||||||||||||||| || | || ||||||||||| || ||||||||
accacacacgcttcaagttcttttaatattctggttatgattaagatttaatcttaagtgttgaagatggtgttaaaggatctattgttctgtttt---------gcagAGAACTTGCTTTTAACTGCAGACCATAAAACAGTAAAACTAGCAGATTTTGGATTAGCAAGAGAAGAGTCACTGACTGAGATGATGACGGCTGAGACAGG
upper sequence: LOC_Os02g38080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G27560.1 (Arabidopsis thaliana), 3'ss of exon 3
tttcttttcagagctatttttttgaaaaaaaatcaagccagaaatatttgtacaaataaggtttatcatgagccattgttttgtccttctgtacgtacagAGAACTTGCTGTTGACCGCAGACCAGAGAACAGTCAAGCTTGTTGACCTTGGTTTAGCAAGAGAAGAGACATTAACAGAGATGATGACTGCAGAGACAGG
| | |||| ||| || | | | | | || || | ||| ||| || || | || | | ||||||| ||| | || | || || || | ||||| || || | ||| | |||||||| |||||||| ||||||| ||||||||||| |||||||| ||
----------------gtaaatggaaagaaatctaaatccgtgacttct----aagtatg---tatggaaagcttatg----atcttattgcatctgcagAGAATTTGATCTTATCAGCGGATCATAAGACAGTGAAACTCGCTGATTTCGGTTTAGCTAGAGAAGAATCATTAACCGAGATGATGACCGCAGAGACTGG
upper sequence: LOC_Os02g38080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G40540.1 (Arabidopsis thaliana), 3'ss of exon 3
tttcttttcagagctatttttttgaaaaaaaatcaagccagaaatatttgtacaaataaggtttatcatgagccattgttttgtccttctgtacgtacagAGAACTTGCTGTTGACCGCAGACCAGAGAACAGTCAAGCTTGTTGACCTTGGTTTAGCAAGAGAAGAGACATTAACAGAGATGATGACTGCAGAGACAGG
| ||| ||| | || |||||| | || || | ||| | || | || || | || | || | | |||||| |||| | || || || || | | || || || || | || |||||||||| |||||||| ||||||| ||||||||||| ||||| || ||
------------gtaattgttt--acaataaatcacacttcaagacattatg-------agttaacaataa--tgttcttatatcttcttggat-tgcagAGAGCTTGATCTTAACTGCGGATTACAAGACTGTTAAACTAGCAGATTTTGGTTTAGCTAGAGAAGAATCATTAACCGAGATGATGACCGCAGAAACTGG
upper sequence: LOC_Os02g38080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv17s0000g09290.t01 (Vitis vinifera), 3'ss of exon 3
tttcttttcagagctatttttttgaaaaaaaatcaagccagaaatatttgtacaaataaggtttatcatg---agccattgttttgtccttctgtacgtacagAGAACTTGCTGTTGACCGCAGACCAGAGAACAGTCAAGCTTGTTGACCTTGGTTTAGCAAGAGAAGAGACATTAACAGAGATGATGACTGCAGAGACAGG
| | | | | | || | || ||| | | ||||| | ||| | || | | | |||| | | | | | | |||||||||| | ||||| |||||||| | |||||| || || || || ||||||||||||| |||||| || | ||||||||||||||||| || |||||
--acatgtttaaaccagttcatagatggtttttcac-tcttacatattgattcaaccagggaagaaattacctatccatgatgggcttccattatttttgcagAGAACTTAATCTTGACTGCAGACCACAAAACAGTTAAACTGGTGGATTTTGGTTTAGCAAGGGAAGAGTCACTGACAGAGATGATGACTGCTGAAACAGG
upper sequence: LOC_Os02g38080.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv14s0066g00370.t01 (Vitis vinifera), 3'ss of exon 3
---tttcttttcaga-gctatttttttgaaaaaaaatcaagccagaaatatttgtacaaataaggtttatcatgagccattgttttgtccttctgtacgtacagAGAACTTGCTGTTGACCGCAGACCAGAGAACAGTCAAGCTTGTTGACCTTGGTTTAGCAAGAGAAGAGACATTAACAGAGATGATGACTGCAGAGACAGG
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gaattatgttttagatgcaaaatatcattgatgaagtgattcccaaaaga--ggcagatatgataataagcttga--caattttttttccttcccttttcccagAAAACTTGATCCTGACTGCAGATCACAAAACTGTCAAACTTGCGGATTTTGGCTTAGCCAGAGAAGAGTCATTAACAGAGATGATGACTGCCGAAACTGGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|84117205|gb|CD150972.1|CD150972EST: CATGGAATGTTTGCATGCGCACCCCATCATTCATCGTGATCTTAAACCTG AGAACTTGCTGTTGACCGCAGACCAGAGAACAGTCAAGCTTGTTGACCTTG
genomic: CATGGAATGTTTGCATGCGCACGCGATCATTCATCGTGATCTTAAACCTGgtaagattgc ... gtacgtacagAGAACTTGCTGTTGACCGCAGACCAGAGAACAGTCAAGCTTGTTGACCTTG
EST:
gi|27576971|gb|CA999665.1|CA999665EST: CATGGAATGTTTGCATGCGCACGCGATCATTCATCGTGATCTTAAACCTG AGAACTTGCTGTTG
genomic: CATGGAATGTTTGCATGCGCACGCGATCATTCATCGTGATCTTAAACCTGgtaagattgc ... gtacgtacagAGAACTTGCTGTTG
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
68 (upstream exon),
68 (downstream exon)
Score:
29AGCCTGGAGCCTCGTGTAGCTGTTGGATTTGCGTTGGATATTGCTCGAGCCATGGAATGTTTGCATGCGCACGCGATCATTCATCGTGATCTTAAACCTGgtaagattgc ... gtacgtacagAGAACTTGCTGTTGACCGCAGACCAGAGAACAGTCAAGCTTGTTGACCTTGGTTTAGCAAGAGAAGAGACATTAACAGAGATGATGACTGCAGAGACAGG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgtacaaataaggtttatcatgagccattgttttgtccttctgtacgtacagAGAACTTGCTGTTGACCGCAGACCAGAGAACAGTCAAGCTTGTTGACCTTGGTTTAGCAAGAGAAGAGACATTAACAGAGATGATGACTGCAGAGACAGG
ttttgtccttctgt CT-rich tract
tacaaataa TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttcttttcagagctatttttttgaaaaaaaatcaagccagaaatatttgtacaaataaggtttatcatgagccattgttttgtccttctgtacgtacagAGAACTTGCTGTTGACCGCAGACCAGAGAACAGTCAAGCTTGTTGACCTTGGTTTAGCAAGAGAAGAGACATTAACAGAGATGATGACTGCAGAGACAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG